Transcriptome Profiling of Lenalidomide Treated Myeloma Patients Identifies an Interferon Signature Gene Response and a Novel IRF4/MYC Independent Mechanism of Resistance

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 170-170
Author(s):  
Paola E. Neri ◽  
Ines Tagoug ◽  
Li Ren ◽  
Ranjan Maity ◽  
Justin Simms ◽  
...  
Keyword(s):  
Cell Line ◽  
Transcriptional Repression ◽  
Sequence Data ◽  
Transcriptome Profiling ◽  
Proteasomal Degradation ◽  
Response To Therapy ◽  
Differentially Expressed ◽  
Interferon Response ◽  
Type I

Abstract Background: Immunomodulatory (IMiDs) drugs are now recognized as modifiers of the degrons targeted by the CLR4-CRBN E3 ligase. Lenalidomide binding to CRBN promotes the proteasomal degradation to the B cell specific zinc finger transcription factors Ikaros (IKZF1) and Aiolos (IKZF3) and the transcriptional repression of IRF4 and MYC. Loss of CRBN thalidomide binding domain as well as the expression of mutants IKZF1Q146H or IKZF3Q147H confer resistance to IMiDs in vitro; however these events are rare in primary MM cells. In addition over-expression of IRF4 only partially protects MM cells from the anti-proliferative effects of IMiDs suggesting that a yet unidentified Aiolos dependent mechanism(s) regulate IMiDs sensitivity. Methods and Results: In order to identify novel mechanisms of resistance to IMiDs we profiled the transcriptome of IMiDs treated patients (sensitive and resistant), MM cell line (MM1S) exposed to lenalidomide and Aiolos silenced MM cells (OPM2). In primary samples, RNA-seq analysis was performed on paired CD138 selected cells sequentially collected from patients’ BM prior to lenalidomide treatment initiation (n=15) and at the time of acquired resistance (n=12) or ongoing response to therapy (n=3). Transcriptome sequence data was generated on the Ion Torrent Proton platform with a minimum of 70x106 reads per sample. Filtered Fastq files were mapped with the TopHat2 splice aligner against hg19. DESeq2 was used to detect differentially expressed (DE) genes. Amongst lenalidomide sensitive patients a total of 870 genes were identified as differentially expressed (FDR <0.1) between the pre- and post-lenalidomide paired samples. Functional annotation of these DE genes using DAVID revealed enrichment of genes involved in immune mediated responses (Gene-Ontology). Of interest interferon γ (IFNγ) was upregulated 3.3 fold in the post-lenalidomide sensitive cohort and 20.4% of the DE genes are type I and II interferon regulated genes (Interferome v2.01). A similar Interferon type of response was also observed in MM1S (Len-sensitive MM cell line) and post Aiolos knockdown of OPM2 cells but not in the lenalidomide resistant cohort. Notably, while several genes that are required for the induction of an interferon response (IL1α, IL1β, TBK1, NLRP3) were upregulated post-lenalidomide in the sensitive cohort, they were downregulated in resistant patients. Of particular interest, two genes that play a key role in modulating IFN response were differentially expressed in the Len resistant cohort: 1) NLRP4 a member of the nucleotide-binding oligomerization domain (NOD)-like receptors (NLRs) was significantly upregulated in lenalidomide resistant patients. NLRP4 negatively regulates type I IFN signaling by targeting the kinase TBK1 for proteasomal degradation and is also recognized to suppress autophagy through Beclin1; 2) NFKBIZ (IkBζ), an atypical IkB kinase required for the induction of IFN response was significantly reduced in lenalidomide-resistant patients. Validation of this lenalidomide induced IFN response was carried out in vitro in MM cells exposed to lenalidomide 10 μM for 24 and 72 hours. A significant increase in IFN stimulated genes (ISGs) such as XAF1, DDX58, IFIT3 was observed following lenalidomide treatment. Similar changes were observed in Aiolos knockdown MM cells. Functionally, silencing of NFKBIZ (through lentiviral shRNA or transient siRNA expression) in MM1S cells resulted in 30% reduction in lenalidomide induced cell death and supressed p21 upregulation but had no effect on the downregulation Aiolos, IRF4 and MYC. Similarly stable overexpression of NLRP4 in MM cells, conferred resistance to lenalidomide. Conclusions: Through comparative transcriptome profiling of lenalidomide resistance and sensitive patients we have identified an Aiolos-dependent induction of interferon stimulated genes as a novel mechanisms of IMiDs mediated cytotoxicity and identified NLRP4 and NFKBIZ as potential mediators of IMiDs resistance. Disclosures Bahlis: Celgene: Honoraria, Research Funding.

scholarly journals Transcriptome analysis ofSchistosoma mansonilarval development using serial analysis of gene expression (SAGE)

Parasitology ◽  
2009 ◽  
Vol 136 (5) ◽  
pp. 469-485 ◽  
Author(s):  
A. S. TAFT ◽  
J. J. VERMEIRE ◽  
J. BERNIER ◽  
S. R. BIRKELAND ◽  
M. J. CIPRIANO ◽  
...  
Keyword(s):  
Gene Expression ◽  
Sequence Data ◽  
Subsequent Development ◽  
Differentially Expressed ◽  
Cdna Libraries ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Expression ◽  
Cell Conditioned Medium

SUMMARYInfection of the snail,Biomphalaria glabrata, by the free-swimming miracidial stage of the human blood fluke,Schistosoma mansoni, and its subsequent development to the parasitic sporocyst stage is critical to establishment of viable infections and continued human transmission. We performed a genome-wide expression analysis of theS. mansonimiracidia and developing sporocyst using Long Serial Analysis of Gene Expression (LongSAGE). Five cDNA libraries were constructed from miracidia andin vitrocultured 6- and 20-day-old sporocysts maintained in sporocyst medium (SM) or in SM conditioned by previous cultivation with cells of theB. glabrataembryonic (Bge) cell line. We generated 21 440 SAGE tags and mapped 13 381 to theS. mansonigene predictions (v4.0e) either by estimating theoretical 3′ UTR lengths or using existing 3′ EST sequence data. Overall, 432 transcripts were found to be differentially expressed amongst all 5 libraries. In total, 172 tags were differentially expressed between miracidia and 6-day conditioned sporocysts and 152 were differentially expressed between miracidia and 6-day unconditioned sporocysts. In addition, 53 and 45 tags, respectively, were differentially expressed in 6-day and 20-day cultured sporocysts, due to the effects of exposure to Bge cell-conditioned medium.

scholarly journals Development of Small-Molecule STING Activators for Cancer Immunotherapy

Biomedicines ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 33
Author(s):  
Hee Ra Jung ◽  
Seongman Jo ◽  
Min Jae Jeon ◽  
Hyelim Lee ◽  
Yeonjeong Chu ◽  
...  
Keyword(s):  
Cancer Immunotherapy ◽  
Cyclic Gmp ◽  
Therapeutic Potential ◽  
Interferon Response ◽  
Type I ◽  
Anti Cancer ◽  
Cancer Agent ◽  
Sting Pathway

In cancer immunotherapy, the cyclic GMP–AMP synthase–stimulator of interferon genes (STING) pathway is an attractive target for switching the tumor immunophenotype from ‘cold’ to ‘hot’ through the activation of the type I interferon response. To develop a new chemical entity for STING activator to improve cyclic GMP-AMP (cGAMP)-induced innate immune response, we identified KAS-08 via the structural modification of DW2282, which was previously reported as an anti-cancer agent with an unknown mechanism. Further investigation revealed that direct STING binding or the enhanced phosphorylation of STING and downstream effectors were responsible for DW2282-or KAS-08-mediated STING activity. Furthermore, KAS-08 was validated as an effective STING pathway activator in vitro and in vivo. The synergistic effect of cGAMP-mediated immunity and efficient anti-cancer effects successfully demonstrated the therapeutic potential of KAS-08 for combination therapy in cancer treatment.

scholarly journals A host type I interferon response is induced by cytosolic sensing of the bacterial second messenger cyclic-di-GMP

2009 ◽  
Vol 206 (9) ◽  
pp. 1899-1911 ◽  
Author(s):  
Sarah M. McWhirter ◽  
Roman Barbalat ◽  
Kathryn M. Monroe ◽  
Mary F. Fontana ◽  
Mamoru Hyodo ◽  
...  
Keyword(s):  
Mammalian Cells ◽  
Map Kinases ◽  
Second Messenger ◽  
Innate Immune ◽  
Guanosine Monophosphate ◽  
Host Cells ◽  
Type I Interferons ◽  
Interferon Response ◽  
Type I

The innate immune system responds to unique molecular signatures that are widely conserved among microbes but that are not normally present in host cells. Compounds that stimulate innate immune pathways may be valuable in the design of novel adjuvants, vaccines, and other immunotherapeutics. The cyclic dinucleotide cyclic-di–guanosine monophosphate (c-di-GMP) is a recently appreciated second messenger that plays critical regulatory roles in many species of bacteria but is not produced by eukaryotic cells. In vivo and in vitro studies have previously suggested that c-di-GMP is a potent immunostimulatory compound recognized by mouse and human cells. We provide evidence that c-di-GMP is sensed in the cytosol of mammalian cells via a novel immunosurveillance pathway. The potency of cytosolic signaling induced by c-di-GMP is comparable to that induced by cytosolic delivery of DNA, and both nucleic acids induce a similar transcriptional profile, including triggering of type I interferons and coregulated genes via induction of TBK1, IRF3, nuclear factor κB, and MAP kinases. However, the cytosolic pathway that senses c-di-GMP appears to be distinct from all known nucleic acid–sensing pathways. Our results suggest a novel mechanism by which host cells can induce an inflammatory response to a widely produced bacterial ligand.

scholarly journals Autophagy Contributes to Host Immunity and Protection against Zika Virus Infection via Type I IFN Signaling

2020 ◽  
Vol 2020 ◽  
pp. 1-15 ◽  
Author(s):  
Yuyi Huang ◽  
Yujie Wang ◽  
Shuhui Meng ◽  
Zhuohang Chen ◽  
Haifan Kong ◽  
...  
Keyword(s):  
Virus Infection ◽  
Cell Line ◽  
Zika Virus ◽  
Fetal Brain ◽  
Host Immunity ◽  
Type I ◽  
Type I Ifn ◽  
Zikv Infection

Recent studies have indicated that the Zika virus (ZIKV) has a significant impact on the fetal brain, and autophagy is contributing to host immune response and defense against virus infection. Here, we demonstrate that ZIKV infection triggered increased LC3 punctuation in mouse monocyte-macrophage cell line (RAW264.7), mouse microglial cell line (BV2), and hindbrain tissues, proving the occurrence of autophagy both in vitro and in vivo. Interestingly, manual intervention of autophagy, like deficiency inhibited by 3-MA, can reduce viral clearance in RAW264.7 cells upon ZIKV infection. Besides, specific siRNA strategy confirmed that autophagy can be activated through Atg7-Atg5 and type I IFN signaling pathway upon ZIKV infection, while knocking down of Atg7 and Atg5 effectively decreased the ZIKV clearance in phagocytes. Furthermore, we analyzed that type I IFN signaling could contribute to autophagic clearance of invaded ZIKV in phagocytes. Taken together, our findings demonstrate that ZIKV-induced autophagy is favorable to activate host immunity, particularly through type I IFN signaling, which participates in host protection and defense against ZIKV infection.

scholarly journals Enhancing innate antiviral immune responses in rainbow trout by double stranded RNA delivered with cationic phytoglycogen nanoparticles

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Tamiru N. Alkie ◽  
Jondavid de Jong ◽  
Kristof Jenik ◽  
Karl M. Klinger ◽  
Stephanie J. DeWitte-Orr
Keyword(s):  
Rainbow Trout ◽  
Immune Responses ◽  
Cell Line ◽  
Culture Conditions ◽  
Type I Interferons ◽  
Poly I:C ◽  
Synthetic Analogue ◽  
Type I ◽  
Viral Dsrna

Abstract Innate immunity is induced when pathogen-associated molecular patterns (PAMPs) bind host pattern recognition receptors (PRRs). Polyinosinic:polycytidylic acid [poly(I:C)] is a synthetic analogue of viral dsRNA that acts as a PAMP, inducing type I interferons (IFNs) in vertebrates. In the present study, the immunostimulatory effects of high molecular weight (HMW) poly(I:C) in rainbow trout cells were measured when bound to a cationic phytoglycogen nanoparticle (Nano-HMW). The physical characteristics of the nanoparticle itself, when bound to different lengths of dsRNA and when cell associated was evaluated. Optimal concentration and timing for innate immune stimulation was measured using the RTG-P1 reporter cell line. The immunostimulatory effects of HMW poly (I:C) was compared to Nano-HMW in vitro using the RTgutGC cell line cultured in a conventional monolayer or a transwell culture system. The ability of an activated intestinal epithelium to transmit an antiviral signal to macrophages was evaluated using a co-culture of RTgutGC cells and RTSll (a monocyte/macrophage cell). In all culture conditions, Nano-HMW was a more effective inducer of IFN-related antiviral immune responses compared to HMW poly (I:C) alone. This study introduces the use of cationic phytoglycogen nanoparticles as a novel delivery system for immunomodulatory molecules to enhance immune responses in aquatic vertebrates.

24 GLOBAL TRANSCRIPT PROFILING OF CLONED BOVINE BLASTOCYSTS USING AFFYMETRIX GENECHIP TECHNOLOGY

2006 ◽  
Vol 18 (2) ◽  
pp. 120
Author(s):  
Z. Beyhan ◽  
P. Ross ◽  
A. Iager ◽  
A. Kocabas ◽  
K. Cunniff ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Expression Profiles ◽  
Cell Structure ◽  
Donor Cell ◽  
Lipid Binding ◽  
Differentially Expressed ◽  
Gtp Binding ◽  
Cloned Bovine

Identification of genes implicated in the biological processes of somatic cell nuclear transfer will improve our understanding of reprogramming events, i.e. the transformation of a lineage-committed cell into a pluripotent one. In addition, the gene expression profile of cloned embryos can help explain the widely reported developmental failures in cloned animals. In this study, we investigated global gene expression profiles of bovine in vitro-fertilized and cloned embryos using Gene Chip Bovine Genome Arrays (Affymetrix, Inc., Santa Clara, CA, USA). For the generation of cloned bovine blastocysts from two adult fibroblast lines (C and D), we employed methods previously proven to generate live offspring and compared these offspring to in vitro-produced blastocysts. Total RNA isolated from groups of 10 blastocysts was amplified by a template-switching PCR. Amplified cDNAs were used to synthesize biotin-labeled antisense RNAs (aRNAs) during and in vitro transcription reaction. Labeled aRNAs were hybridized to microarrays as described by the manufacturer. Experiments were performed in four replicates. Expression data were analyzed using the Significance Analysis of Microarrays (SAM; Tusher et al. 2001 Proc. Natl. Acad. Sci. 98, 5116-5121) procedure and software. Overall, 48.4% and 46% of 23 000 bovine transcripts spotted on the arrays were present in cloned and in in vitro-produced control blastocysts, respectively. The SAM procedure identified 43 genes that changed at least 1.5-fold, with an estimated false discovery rate (FDR) of 20%. Comparison of gene expression between NT embryos produced from two different cell lines and IVF controls with the same criteria revealed 6 (clones from cell line C vs. IVF) and 46 (clones from cell line D vs. IVF) differentially expressed genes. The number of transcripts expressed differentially between the cloned embryos with different donor cell origin was 437. Of the 43 differentially expressed transcripts in cloned blastocysts, 13 have unknown functions and the rest of the genes related to cell structure (tuftelin, desmoplakin), cell cycle/mitosis (Kinesin like 4, katanin, stathmin, PCNA), energy metabolism (lactate dehydrogenase, ATPsynthase, lipid-binding protein, keto acid dehydrogenase E1, metallothionein), and cell signaling (GTP-binding protein1, GTP binding stimulatory protein). Our results indicate that expression profiles of cloned blastocysts could be affected by somatic donor cell.

scholarly journals Equid Herpesvirus 1 Targets the Sensitization and Induction Steps To Inhibit the Type I Interferon Response in Equine Endothelial Cells

2019 ◽  
Vol 93 (23) ◽  
Author(s):  
Fatai S. Oladunni ◽  
Sanjay Sarkar ◽  
Stephanie Reedy ◽  
Udeni B. R. Balasuriya ◽  
David W. Horohov ◽  
...  
Keyword(s):  
Endothelial Cells ◽  
Cellular Level ◽  
Immune Defense ◽  
Interferon Response ◽  
Type I ◽  
Type I Ifn ◽  
Viral Pathogen ◽  
Equid Herpesvirus ◽  
Herpesvirus 1

ABSTRACT Equid herpesvirus 1 (EHV-1) is a viral pathogen of horse populations worldwide spread by the respiratory route and is known for causing outbreaks of neurologic syndromes and abortion storms. Previously, we demonstrated that an EHV-1 strain of the neuropathogenic genotype, T953, downregulates the beta interferon (IFN-β) response in vitro in equine endothelial cells (EECs) at 12 h postinfection (hpi). In the present study, we explored the molecular correlates of this inhibition as clues toward an understanding of the mechanism. Data from our study revealed that EHV-1 infection of EECs significantly reduced both Toll-like receptor 3 (TLR3) and TLR4 mRNA expression at 6 hpi and 12 hpi. While EHV-1 was able to significantly reduce IRF9 mRNA at both 6 hpi and 12 hpi, the virus significantly reduced IFN regulatory factor 7 (IRF7) mRNA only at 12 hpi. EHV-1 did not alter the cellular level of Janus-activated kinase 1 (JAK1) at any time point. However, EHV-1 reduced the cellular level of expression of tyrosine kinase 2 (TYK2) at 12 hpi. Downstream of JAK1-TYK2 signaling, EHV-1 blocked the phosphorylation and activation of signal transducer and activator of transcription 2 (STAT2) when coincubated with exogenous IFN, at 12 hpi, although not at 3 or 6 hpi. Immunofluorescence staining revealed that the virus prevented the nuclear translocation of STAT2 molecules, confirming the virus-mediated inhibition of STAT2 activation. The pattern of suppression of phosphorylation of STAT2 by EHV-1 implicated viral late gene expression. These data help illuminate how EHV-1 strategically inhibits the host innate immune defense by limiting steps required for type I IFN sensitization and induction. IMPORTANCE To date, no commercial vaccine label has a claim to be fully protective against the diseases caused by equid herpesvirus 1 (EHV-1), especially the neurologic form. The interferon (IFN) system, of which type I IFN is of great importance, still remains a viable immunotherapeutic option against EHV-1 infection. The type I IFN system has been exploited successfully to treat other viral infections, such as chronic hepatitis B and C in humans. The current state of research on how EHV-1 interferes with the protective effect of type I IFN has indicated transient induction of type I IFN production followed by a rapid shutdown in vitro in equine endothelial cells (EECs). The significance of our study is the identification of certain steps in the type I IFN signaling pathway targeted for inhibition by EHV-1. Understanding this pathogen-host relationship is essential for the long-term goal of developing effective immunotherapy against EHV-1.

Identification of a CpG Island in the Human LRP-2 Gene and Analysis of Its Methylation Status in Parathyroid Adenomas

2000 ◽  
Vol 381 (5-6) ◽  
pp. 433-438 ◽  
Author(s):  
A. Knutson ◽  
P. Lillhager ◽  
G. Westin
Keyword(s):  
Cell Line ◽  
Transcriptional Repression ◽  
Cpg Island ◽  
Methylation Status ◽  
Parathyroid Tissue ◽  
Cellular Functions ◽  
Gene Encoding ◽  
Parathyroid Adenomas ◽  
Multiple Ligands

Abstract Methylation of CpG residues in mammalian genomes is a mechanism of vital importance for many cellular functions, which all relate to gene expression. In this study we describe the identification of a CpG island in the 5′-region of the gene encoding human megalin/LRP-2, a receptor capable of binding multiple ligands, which is involved in the regulation of calcium metabolism. Southern blot analysis and genomic bisulfite sequencing revealed that the CpG island is methylated in a non-expressing cell line, largely unmethylated in an expressing cell line and unmethylated in human parathyroid tissue. In addition, we show that artificial methylation of LRP-2 promoter reporter plasmids leads to strong transcriptional repression, in vitro as well as in transfected cells. No evidence for aberrant LRP-2 gene methylation in parathyroid adenomas, in which the LRP-2 protein is generally down-regulated, was found.

scholarly journals Interferon Regulatory Factor IRF-7 Induces the Antiviral Alpha Interferon Response and Protects against Lethal West Nile Virus Infection

2008 ◽  
Vol 82 (17) ◽  
pp. 8465-8475 ◽  
Author(s):  
Stephane Daffis ◽  
Melanie A. Samuel ◽  
Mehul S. Suthar ◽  
Brian C. Keller ◽  
Michael Gale ◽  
...  
Keyword(s):  
West Nile Virus ◽  
Cortical Neurons ◽  
Interferon Regulatory Factor ◽  
Interferon Response ◽  
Type I ◽  
Type I Ifn ◽  
Regulatory Factor ◽  
West Nile

ABSTRACT Type I interferon (IFN-α/β) comprises a family of immunomodulatory cytokines that are critical for controlling viral infections. In cell culture, many RNA viruses trigger IFN responses through the binding of RNA recognition molecules (RIG-I, MDA5, and TLR-3) and induction of interferon regulatory factor IRF-3-dependent gene transcription. Recent studies with West Nile virus (WNV) have shown that type I IFN is essential for restricting infection and that a deficiency of IRF-3 results in enhanced lethality. However, IRF-3 was not required for optimal systemic IFN production in vivo or in vitro in macrophages. To begin to define the transcriptional factors that regulate type I IFN after WNV infection, we evaluated IFN induction and virus control in IRF-7−/− mice. Compared to congenic wild-type mice, IRF-7−/− mice showed increased lethality after WNV infection and developed early and elevated WNV burdens in both peripheral and central nervous system tissues. As a correlate, a deficiency of IRF-7 blunted the systemic type I IFN response in mice. Consistent with this, IFN-α gene expression and protein production were reduced and viral titers were increased in IRF-7−/− primary macrophages, fibroblasts, dendritic cells, and cortical neurons. In contrast, in these cells the IFN-β response remained largely intact. Our data suggest that the early protective IFN-α response against WNV occurs through an IRF-7-dependent transcriptional signal.

scholarly journals CX-5461 Treatment Leads to Cytosolic DNA-Mediated STING Activation in Ovarian Cancer

Cancers ◽  
2021 ◽  
Vol 13 (20) ◽  
pp. 5056
Author(s):  
Robert Cornelison ◽  
Kuntal Biswas ◽  
Danielle C. Llaneza ◽  
Alexandra R. Harris ◽  
Nisha G. Sosale ◽  
...  
Keyword(s):  
Ovarian Cancer ◽  
Time Frame ◽  
Interferon Response ◽  
Type I ◽  
Pol I ◽  
Downstream Effects ◽  
Immune Pathway ◽  
Polymerase I

Epithelial ovarian cancer (EOC) is the deadliest of the gynecologic malignancies, with an overall survival rate of <30%. Recent research has suggested that targeting RNA polymerase I (POL I) with small-molecule inhibitors may be a viable therapeutic approach to combating EOC, even when chemoresistance is present. CX-5461 is one of the most promising POL I inhibitors currently being investigated, and previous reports have shown that CX-5461 treatment induces DNA damage response (DDR) through ATM/ATR kinase. Investigation into downstream effects of CX-5461 led us to uncovering a previously unreported phenotype. Treatment with CX-5461 induces a rapid accumulation of cytosolic DNA. This accumulation leads to transcriptional upregulation of ‘STimulator of Interferon Genes’ (STING) in the same time frame, phosphorylation of IRF3, and activation of type I interferon response both in vitro and in vivo. This activation is mediated and dependent on cyclic GMP–AMP synthase (cGAS). Here, we show THAT CX-5461 leads to an accumulation of cytosolic dsDNA and thereby activates the cGAS–STING–TBK1–IRF3 innate immune pathway, which induces type I IFN. CX-5461 treatment-mediated immune activation may be a powerful mechanism of action to exploit, leading to novel drug combinations with a chance of increasing immunotherapy efficacy, possibly with some cancer specificity limiting deleterious toxicities.

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